184 lines
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HTML
184 lines
18 KiB
HTML
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<nav class="ncbi-topnav">
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<ul class="ncbi-topnav-list">
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<li><a href="." target="_self">NCBI Sequence Viewer Home</a></li>
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<li><a href="/tools/sviewer" target="_blank">Help</a></li>
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<li><a href="/tools/sviewer/release-notes" target="_blank">Release Notes</a></li>
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<h1>Example cases for coordinate reporting</h1>
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<p>
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The NCBI Graphical Sequence Viewer (SV) is a tool for viewing biological sequence data. Following are embedded examples of the viewer with markers indicating a particular position on the sequence. To set your own marker, right-click in Sequence Viewer on the desired position and click on the menu item "Set New Marker at Position". To see additional details of the marked position, right-click on the marker and select "Marker Details".
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</p>
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<p>The <a href="https://varnomen.hgvs.org/" target="_blank">HGVS</a> name is reported in the marker details table.
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To view examples of searching by HGVS, refer to the <a href="HGVSDemo.html">HGVS and SNP Search</a> demo page.
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</p>
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<ol class="sv-indent">
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<li class="sv-indent">
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NC_000007.14: Homo sapiens chromosome 7, GRCh38.p12 Primary Assembly.<br/>
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Gene, mRNA, and CDS are shown. Marker is right after stop codon for NP_775788.2 and XP_011514133.1.<br/>
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<a href="https://go.usa.gov/xmGJZ" target="_blank">Link to embedded view with opened marker details table</a><br/><br/>
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<div class="SeqViewer">
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<div id="SeqViewer1" class="SeqViewerApp" data-autoload>
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<a href="?embedded=true&appname=markerdemo&id=NC_000007.14&tracks=[key:sequence_track,name:T15993,display_name:Sequence,id:T15993,dbname:GenBank,category:Sequence,subcategory:Assembly,annots:Sequence,ShowLabel:false,shown:true,order:9][key:gene_model_track,name:T1470661,display_name:Genes\,%20NCBI%20Homo%20sapiens%20Annotation%20Release%20109\,%202018-03-27,id:T1470661,dbname:SADB,category:Genes,subcategory:NCBI%20Genes,annots:NA000152403.1,Options:ShowAll,SNPs:false,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:86]&assm_context=GCF_000001405.38&mk=65954301|Marker%201|008000&v=65954245:65954322&c=ff6600&select=gi|568815591-03ed082b-03ee768a-0101-96a1089b-ffea8d58"></a>
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</div>
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</div></li>
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<li class="sv-indent">
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NG_005895.1: Homo sapiens TSC complex subunit 2 (TSC2), RefSeqGene (LRG_487) on chromosome 16.<br/>
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Marker is at the end of the first non-coding exon<br/>
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<a href="https://go.usa.gov/xmGJN" target="_blank">Link to embedded view with opened marker details table;</a><br/>
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notice that the table shows marked positions relative to RefSeq transcript alignments.<br/><br/>
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<div class="SeqViewer">
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<div id="SeqViewer2" class="SeqViewerApp" data-autoload>
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<a href="?embedded=true&appname=markerdemo&id=NG_005895&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:gene_model_track,name:Genes,display_name:Genes,id:STD3194982005,category:Genes,annots:Unnamed,Options:ShowAll,SNPs:true,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:5][key:alignment_track,name:Alignments,display_name:Alignments%20-%20Reference%20transcript%20alignments,id:STD1042840653,category:Alignments,annots:Reference%20transcript%20alignments,Layout:Adaptive,StatDisplay:15,Color:Show%20Differences,UnalignedTailsMode:glyph,sort_by:,LinkMatePairAligns:false,ShowAlnStat:false,AlignedSeqFeats:false,Label:true,IdenticalBases:false,shown:true,order:6]&mk=3761|Marker%201|008000&v=3624:4767"></a>
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</div>
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</div>
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</li>
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<li class="sv-indent">
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NC_000019.9 Homo sapiens chromosome 19, GRCh37.p13 Primary Assembly. Gene CEACAM20; marker at the indel position.<br/>
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The RefSeq transcripts/proteins have a 1 nt deletion relative to the genomic sequence (forward ribosomal slippage, minus strand)<br/>
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<a href="https://go.usa.gov/xmGJE" target="_blank">Link to embedded view with opened marker details table</a><br/><br/>
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<div class="SeqViewer">
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<div id="SeqViewer3" class="SeqViewerApp" data-autoload>
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<a href="?embedded=true&appname=markerdemo&id=NC_000019.9&tracks=[key:sequence_track,name:T16507,display_name:Sequence,id:T16507,dbname:SADB,annots:NA000001672.2,ShowLabel:false,ColorGaps:false,shown:true,order:1][key:gene_model_track,name:T2000262,display_name:Genes\,%20NCBI%20Homo%20sapiens%20Annotation%20Release%20105.20190906,id:T2000262,dbname:SADB,annots:NA000229419.1,Options:ShowAll,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,ShowLabel:true,shown:true,order:18]&assm_context=GCF_000001405.13&mk=45016991|Marker%201|0000ff&v=45016963:45017017"></a>
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</div>
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</div>
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</li>
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<li class="sv-indent">
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NC_000019.9 Homo sapiens chromosome 19, GRCh37.p13 Primary Assembly.
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Gene LTBP4; marker at the indel position.<br/>
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The RefSeq transcripts/proteins have a 1 nt insertion relative to the genomic sequence (backward ribosomal slippage, plus strand)<br/>
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<a href="https://www.ncbi.nlm.nih.gov/nuccore/224589810?report=graph&tracks=[key:sequence_track,name:T16507,display_name:Sequence,id:T16507,dbname:SADB,category:Sequence,subcategory:Assembly,annots:NA000001672.2,ShowLabel:false,shown:true,order:5][key:gene_model_track,name:T11201,display_name:Genes\, NCBI Homo sapiens Annotation Release 105,id:T11201,dbname:SADB,category:Genes,subcategory:NCBI Genes,annots:NA000009701.1,Options:ShowAll,SNPs:false,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:21]&assm_context=GCF_000001405.13&mk=41123095|Marker%201|008000&vm=true&v=41123053:41123171&select=gi|224589810-02733f5d-0273ad5e-0103-027cbd31-ffea8d58" target="_blank">Link to embedded view with opened marker details table</a><br/><br/>
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<div class="SeqViewer">
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<div id="SeqViewer4" class="SeqViewerApp" data-autoload>
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<a href="?embedded=true&appname=markerdemo&id=NC_000019.9&tracks=[key:sequence_track,name:T16507,display_name:Sequence,id:T16507,dbname:SADB,annots:NA000001672.2,ShowLabel:false,ColorGaps:false,shown:true,order:1][key:gene_model_track,name:T2000262,display_name:Genes\,%20NCBI%20Homo%20sapiens%20Annotation%20Release%20105.20190906,id:T2000262,dbname:SADB,annots:NA000229419.1,Options:ShowAll,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,ShowLabel:true,shown:true,order:18]&assm_context=GCF_000001405.13&mk=41123095:41123096|Marker%201|blue&v=41123067:41123121"></a>
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</div>
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</div>
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</li>
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<li class="sv-indent">
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NC_024459.1: Zea mays cultivar B73 chromosome 1, B73 RefGen_v3<br/>
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Markers are at the deletion, insertion, and mismatch in RefSeq transcripts compared to the genomic sequence<br/>
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<a href="https://go.usa.gov/xmGSn" target="_blank">Link to embedded view with opened marker details table</a><br/><br/>
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<div class="SeqViewer">
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<div id="SeqViewer5" class="SeqViewerApp" data-autoload>
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<a href="?embedded=true&appname=markerdemo&id=NC_024459.1&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:499][key:gene_model_track,name:Genes,display_name:Genes,id:STD3194982005,category:Genes,annots:Unnamed,Options:ShowAll,SNPs:false,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:500][key:alignment_track,name:Alignments,display_name:Refseq%20Alignments,id:STD4244105117,category:Alignments,annots:Refseq%20Alignments,Layout:Adaptive,StatDisplay:15,Color:Show%20Differences,UnalignedTailsMode:glyph,sort_by:,LinkMatePairAligns:true,ShowAlnStat:false,AlignedSeqFeats:true,Label:true,IdenticalBases:false,shown:true,order:501][key:feature_track,name:STS%20Markers,display_name:STS%20Markers,id:STD839026914,subkey:STS,category:Features,subcategory:STS%20Markers,annots:STS,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:502]&assm_context=GCF_000005005.1&mk=5738492:5738497|Deletion|008000,5738508:5738509|Insertion|0000ff,5738525:5738525|Mismatch|ff0000&v=5738473:5738553&c=333300&select=gi|662250330-00578fca-00579a6c-010a-7de718e6-ffea8d58"></a>
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</div>
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</div>
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</li>
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<li class="sv-indent">
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NC_000008.11 Homo sapiens chromosome 8, GRCh38.p12 Primary Assembly.
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Marker is at the SNP rs41276297 position.<br/>
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<a href="https://go.usa.gov/xmGWP" target="_blank">Link to embedded view with opened marker details table</a><br/>
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<div class="SeqViewer">
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<div id="SeqViewer6" class="SeqViewerApp" data-autoload>
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<a href="?embedded=true&appname=markerdemo&id=NC_000008.11&tracks=[key:sequence_track,name:T15993,display_name:Sequence,id:T15993,dbname:GenBank,category:Sequence,subcategory:Assembly,annots:Sequence,ShowLabel:false,shown:true,order:9][key:gene_model_track,name:T1470661,display_name:Genes\,%20NCBI%20Homo%20sapiens%20Annotation%20Release%20109\,%202018-03-27,id:T1470661,dbname:SADB,category:Genes,subcategory:NCBI%20Genes,annots:NA000152403.1,Options:ShowAll,SNPs:false,CDSProductFeats:false,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:86][key:SNP_track,name:T1715723,display_name:Cited%20Variations\,%20dbSNP%20b152%20v2,id:T1715723,dbname:VDB,category:Variation,subcategory:dbSNP%20Build%20152%20(Homo%20sapiens%20Annotation%20Release%20109),annots:NA000193272.1\232,Layout:Adaptive,shown:true,order:121][key:SNP_track,name:T1715724,display_name:Clinical\,%20dbSNP%20b152%20v2,id:T1715724,dbname:VDB,category:Variation,subcategory:dbSNP%20Build%20152%20(Homo%20sapiens%20Annotation%20Release%20109),annots:NA000193272.1\2320,Layout:Adaptive,shown:true,order:124]&assm_context=GCF_000001405.38&mk=27605145:27605145|Marker%201|green&v=27605089:27605192&c=CC99FF&select=gi|568815590-01a51874-01a55f36-0101-2cf04050-ffea8d58"></a>
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</div>
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</div>
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</li>
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<li class="sv-indent">
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NM_002020.4 Homo sapiens fms related tyrosine kinase 4 (FLT4), transcript variant 2, mRNA.<br/>
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Marker is located at position 1513 relative to the start of NM_002020.4 and corresponds to position 1434 on the CDS and position 478 on the encoded protein NP_002011.2<br/>
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<a href="https://go.usa.gov/xmaDJ" target="_blank">Link to embedded view with opened marker details table</a><br/>
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<div class="SeqViewer">
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<div id="SeqViewer7" class="SeqViewerApp" data-autoload>
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<a href="?embedded=true&appname=markerdemo&id=NM_002020&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:gene_model_track,name:Genes,display_name:Genes,id:STD3194982005,category:Genes,annots:Unnamed,Options:ShowAll,SNPs:false,CDSProductFeats:true,NtRuler:true,AaRuler:true,HighlightMode:2,shown:true,order:3][key:feature_track,name:STS%20Markers,display_name:STS%20Markers,id:STD839026914,subkey:STS,category:Features,subcategory:STS%20Markers,annots:STS,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:4]&mk=1513|Marker%201|008000&v=1:4534&c=00ff00"></a>
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</div>
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</div>
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</li>
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<li class="sv-indent">
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NP_000928.1 DNA-directed RNA polymerase II subunit RPB1 [Homo sapiens].<br/>
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Marker is located at position 773 relative to the start of NP_000928.1<br/>
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<a href="https://go.usa.gov/xmaWY" target="_blank">Link to embedded view with opened marker details table</a><br/>
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<div class="SeqViewer">
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<div id="SeqViewer8" class="SeqViewerApp" data-autoload>
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<a href="?embedded=true&appname=markerdemo&id=4505939&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD649220238,category:Sequence,annots:Sequence,ShowLabel:false,shown:true,order:1][key:feature_track,name:Other%20features---Protein,display_name:Protein%20Features,id:STD2439759237,subkey:Prot,category:Features,subcategory:Protein%20Features,annots:Unnamed,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:2][key:feature_track,name:Other%20features---region---CDD,display_name:region%20Features%20-%20CDD,id:STD361885503,subkey:region,category:Features,subcategory:region%20Features,annots:CDD,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:3][key:feature_track,name:Other%20features---region---Unnamed,display_name:region%20Features,id:STD408713146,subkey:region,category:Features,subcategory:region%20Features,annots:Unnamed,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:4][key:feature_track,name:Other%20features---site---CDD,display_name:site%20Features%20-%20CDD,id:STD2917610742,subkey:site,category:Features,subcategory:site%20Features,annots:CDD,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:5][key:feature_track,name:Other%20features---site---Unnamed,display_name:site%20Features,id:STD2492180595,subkey:site,category:Features,subcategory:site%20Features,annots:Unnamed,Layout:Adaptive,LinkedFeat:Packed,shown:true,order:6][key:SNP_track,name:T1716514,display_name:Cited%20Variations\,%20dbSNP%20b152%20v2,id:T1716514,dbname:VDB,category:Variation,subcategory:dbSNP,annots:NA000146873.10\232,Layout:Adaptive,shown:true,order:7]&mk=773|Marker%201|008000&v=722:828"></a>
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</li>
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</ol>
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